The story begins at the Midair Stadium. The tournament is hosted by Yoshi and Peach, who wave at the applauding crowd.

Mario emerges from one side of the stadium, and Luigi, the other. They battle, and based on who you picked, Mario or Luigi wins.

After Mario and Luigi high-five and wave to the crowd, the sky suddenly becomes dark. Giygas's Mother Ship emerges from over the stadium. A hatch under the ship opens, and a large water tank falls to the battle field. Giygas shows himself from within the dark water. Then Count Bleck appears. Giygas plants a bomb in the center of the stadium, and Yoshi and Peach come down to help Mario and Luigi fight Count Bleck. They defeat Count Bleck. Then, Yubel appears and snatches Yoshi, and Giygas snatches Peach. Mario and Luigi try to save them, but arent successful. Then Count Bleck pulls out the Dark Prognosticus, and summons The Void off in the distance. Then he laughs maniacally before disappearing. Giygas and Yubel fly back up to the Mother Ship, which flies away.

Mario and Luigi escape on Sky Pops before the bomb explodes, destroying the stadium. They pursue the Mother Ship.

Meanwhile, off in The Arcane Forrest, Krystal walks into a room in the temple, and finds an ancient Krazoa artifact on a pedestal. Before she is able to grab it, Indiana Jones uses his whip to grab the artifact. Krystal gets mad and they fight.

After the fight, Indy runs away with the Krazoa artifact. After running through the forest for a while, he runs into a herd of Bulborbs. Overhead, the Mother Ship flies overhead while it shoots at Mario and Luigi’s Sky Pops. They are shot down, and they crash on the Bulborbs. They meet Indy and they all run into the forest.

Meanwhile, Link investigates the ruins of Castle Olrox. He stumbles upon a shrine devoted to Dracula. Nathan Graves appears and, mistaking Link for a follower of Dracula, attacks.

After they fight, Nathan turns Link into Wolf Link, but learns that he is not an enemy. Then they are ambushed by monsters commanded by Mr. Dark. They try to fight, but Mr. Dark defeats them with ease. Nathan and Wolf Link pursue Mr. Dark.

In the Mother Ship, Giygas and Yubel bring Peach and Yoshi to Ganondorf. He commands that they both be turned into trophies, but Yoshi be thrown overboard. Peach and Yoshi are turned into trophies and Yubel throws Yoshi overboard.

Meanwhile, back in The Arcane Forest, Mario, Luigi, and Indy enter the Begoniax Swamp. After fighting through Darkness Soldiers, they battle The Giant Fly deep in the swamp. After the fly is dead, two Darkness Soldiers activate a Darkness Bomb, engulfing the Forest in Darkness. But Mario, Luigi, and Indy escape in time.

Back in the temple, Fox and Falco find Krystal's trophy and returns her back to normal. They both leave the temple and find the whole forest encased in Darkness. Krystal uses her telepathy to track Indiana. Finding his trail, Krystal, Fox, and Falco chase after them.

Back in Castle Olrox, Nathan and Wolf Link continue chasing Mr. Dark, who carries a Darkness Bomb. Mr. Dark prepairs to activate it, but Simon appears and uses his whip to knock it from his hands, destroying the bomb. Mr. Dark escapes to the Mother Ship.

Meanwhile, in the Beanstalk Way, Donkey Kong and Diddy Kong are exploring the area. Suddenly Yoshi's trophy falls from the sky and the Mother Ship passes overhead, dispensing soldiers into the area. Diddy turns Yoshi back to normal and the team up to fight the soldiers. In the Beanstalk Way Valley, they see Mario, Luigi, and Indy being chased by Fox, Falco, and Krystal. Fox and Falco shoot at the trio, while Indy shoots back. DK, Diddy and Yoshi intervene between the groups. They settle their differences, and they all team up to fight the Darkness Soldiers. However, Andross appears with Count Bleck. They turn Fox, Falco, Krystal, Diddy, and DK into trophies. They take them away. In a nearby grove, Kirby and Lucario witness what happened, and, while chasing Andross and Bleck, they meet Mario, Luigi, Indy, and Yoshi. While pursuing Andross and Bleck, they come across the King Piranha, and become side tracked while fighting. They loose Andross and Bleck. Andross shoots the Beanstalk Way with his finger, and plunges it into Darkness. Meanwhile The Void gets bigger.

In the Mountains, Sonic, Tails, and Shadow are investigating the strange occurences in the area. They come across a small rift in the mountain. Shadow warns Sonic that it might be dangerous, but Sonic doesn't listen. Staring directly into it, he becomes hypnotised by the portal. When the portal snaps shut, he transforms into Sonic the Werehog. Seeing his friends as food, he attacks. After Tails and Shadow defeat him, Shadow taps his trophy and turns him back to normal. Still the Werehog, he prepares to attack again, but Shadow punches him in the face, returning him to his senses. Nathan, Simon, and Wolf Link run into them, and they all team up. Dr. Eggman, however, appears and turns Sonic into a trophy and snatches him. The group run after him.

Meanwhile, Ike, Roy, and Marth and doing a little sword training in an ancient castle. The sword play becomes a little rough and Roy is shot through a wall, into Mewtwo's meditation room. Angered by their presence, he attacks. The swordsman easily overwhelm him and defeat him. Renamon, Mewtwo's girlfriend, steps in to see the three defeat Mewtwo. She becomes furious and attacks them, but she is defeated as well. As Ike turns them back to normal, Roy hears something. Roy silences Mewtwo and Renamon's bantering, and the noise becomes a little louder. Suddenly the wall explodes and Bowser and his minions attack. The five fight the Darkness Soldiers, but Bowser shoots Mewtwo with a ray gun, copying his DNA and creating Mewtwo's Doppelganger. Bowser and the Doppelganger simply run away, leaving the group confused.

Eggman takes Sonic to a factory to create Metal Sonic the Werehog, which is being overseen by Liquid Ocelot. Eggman takes him to a room where Sonic is attached to a bunch of machinery. The creation of Metal Sonic begins.

Almost everyone in the factory is watching the transformation, so Old Snake easily breaks in. Looking for Liquid, he manages to through all the traps and interupts the Metal Sonic creation. He turns Sonic back to normal. He breaks from his binds, and Metal Sonic is left incomplete. Liquid orders Eggman to stop them while he escapes. Eggman is defeated by Sonc and Old Snake, but Metal Sonic awakens and attacks. Metal Sonic is defeated, but he pulls out a Darkness Bomb. Old Snake and Sonic escape and are saved by Samus before the factory is consumed by Darkness. In the ship, Samus introduces Snake and Sonic to Anakin Skywalker, who is helping her on a mission. Old Snake types cordinates into Samus's computer, and locates Liquid's ship. They pursue Liquid, who has trophies of Zelda, Olimar, and Mr. Game & Watch in the cargo hold.

Nathan, Simon, and the others are looking for where Eggman went. They come across a graveyard, that Simon recognizes. He and Nathan step through the gate to make sure it's safe, but when they do, the gate slams shut, locking them inside. Tails and Shadow are locked outside, and Nathan and Simon are forced to find another way out.

After braving many undead creatures that plague the graveyard, they come across the grave of Leon Belmont, Simon's ancestor. Examining the grave, Simon senses something strange. Leon's ghost suddenly appears behind them, but Simon's quick thinkng saves him and Nathan. They fight the ghost, and soon learn that it was a fake conjured up by Dry Bowser, who stands at the entrance to the catacombs. He laughs at them, and flees to the underground graves. Simon and Nathan chase after him.

After fighting through the catacombs, Nathan and Simon corner Dry Bowser in his lair. They fight Dry Bowser and soon defeat him. Simon turns him back to normal. When Dry Bowser was about to attack again, Mr. Dark and his minions suddenly appear, and turns Simon into a trophy. Mr. Dark snatches him. Nathan and Dry Bowser chase after Mr. Dark once again, forgetting that he left Tails and Shadow behind.

Back outside the gate to the graveyard, Shadow and Tails are still waiting for Nathan and Simon to come back. Tails wants to wait for them, but Shadow is convinced that they are dead. So they leave the graveyard and go elsewhere to look for Sonic. But then Tails realizes something: Where is Wolf Link?

Wolf Link, who got seperated from Simon and Nathan, takes a drink from the lake. Then Big Squiddy appears from beneath the waters and attacks him.

Meanwhile, back with Mario, Luigi, Indy, Yoshi, Lucario, and Kirby, they are walking around, still looking for Andross and Bleck. Lucario picks up a noise coming from the lake. They go investigate, and find Wolf Link, half-beaten to death by Big Squiddy, who laughs at his attempts to stand. Mario and co. attack Big Squiddy, but right when Big Squiddy almost defeats them, Mewtwo, Renamon, and the three swordsman step in and save them. Big Squiddy sinks back down below the lake. Renamon tends to Wolf Links wounds while the others discuss what has been happening.

In the Mother Ship, Yubel and Ganondorf spy over the land. Spotting Mario and his friends, she commands Giygas to go after them. She also sends Bowser and Mewtwo's Doppelganger with them.

Meanwhile, Samus, Old Snake, Anakin, and Sonic are still chasing Liquid. Inside Liquids ship, Liquid smiles triumphantly, thinking he's going to get away. But from within the back of his ship, Wolf emerges from the darkness. Quietly walking into the cockpit, he hits Liquid upside the head, knocking him out. Throwing Liquid aside, he takes control of the ship, enters data into the navacomputer, and locates Andross. Turning the ship around, he flies to Andross. A confused Samus turns her ship around and follows.

Back at the lake, the whole group is talking, but the a beam of light hits Mewtwo and turns him into a trophy. The group looks and sees Giygas, Bowser, and Mewtwo's Doppelganger. Bowser laughs at them. Giygas uses a mechanical arm from his water tank to snatch Mewtwo. Giygas and Bowser leave with Mewtwo, while his Doppelganger stays and fights. They fight Mewtwo's clone, and destroy him. In a fit of rage, Renamon gets a head start after them. The others follow after her.

Wolf locates Andross, who is still with Count Bleck. Wolf fights Andross, with the help of Samus and the others. Together they destroy Andross, who drops his load of trophies. Wolf glides his ship under the trophies, but before he is able to open the hatch and let them in, Liquid wakes up, yanks Wolf from the controls, which sends the ship spiraling out of control, and they fight.

In the aftermath of the fight, Wolf throws Liquid against the control panel, which causes him to open the cargo hold, dumping everything into the air, including the three trophies. Liquid grabs Wolf and throws him through the cockpit window. Wolf manages to grab onto the front of the ship, and uses his claws to climb back up to the cockpit. Liquid tries to throw him back out, but Wolf pulls out his blaster and shoots the button that opens the escape pod at the other end of the ship. He launches himself into the cockpit, knocks Liquid out of the way, and runs for the escape pod. Once inside, he presses the button to eject the pod, but before the door closes, Liquid pulls out his gun and shoots Wolf in the shoulder. The escape pod shoots from the ship. Liquid runs over to the controls, and resets the destination of the escape pod to the Mother Ship. Liquid chuckles to himself, and the ship's power dies. With nothing powering it, the ship plumets to the earth and explodes.

Seeing the escape pod veer of in a different direction, and thinking it's Liquid, Old Snake follows the pod.

Meanwhile on the Mother Ship, Wario, who is a mechanic, is repairing a bunch of stuff. He picks up a load of boxes and takes it into a dimly lit room. In the center of the room is a large stasis tank with a sleeping Megaman inside. Wario passes by the tank, trips and makes a lot of noise, waking Megaman. As Wario picks up the stuff he dropped, he accidentally backs up into the control panel, emptying the tank. Megaman blasts through the tank, setting off the alarm. As he gets out, Darkness Soldiers burst into the room. Megaman becons for Wario to help him.

Mario and the others are still chasing Giygas and Bowser. With the help of Kirby, Renamon launches herself at them, and taps Mewtwo's trophy, also breaking the glass on Giygas's tank. Giygas panickingly flees back to the Mother Ship to repair his tank. Bowser stops to fight them, only to loose. This time the leave Bowser's trophy behind. Not knowing where else to go, they go check out the nearby Castle Olrox.

While Shadow and Tails are still walking around, they come across the trophies of DK and Diddy Kong. Shadow revives them, and they join forces. Out the corner of his eye, Tails sees Nathan and Dry Bowser chasing after Mr. Dark, carrying Simon's trophy. They join the chase, and Shadow pull out his blaster and shoots the trophy out of Mr. Dark's hand. Mr. Dark flees. Nathan reluctantly revives Simon.

While Mario's group rests in Castle Olrox, Indy takes the Krazoa artifact he found out of his pack and puts it on the floor. Wolf Link comes over, smells it, and touches it with his paw. The second he does, he turns back into Link. The nearby Darkness Soldiers sense the artifacts power and ambush the group.

Wolf's escape pod crashes into the side of the Mother Ship. He gets out and investigates. After a while, he runs into Megaman and Wario, and they team up, but not before they go back to the medical bay to fix Wolf's bloody shoulder.

Deep inside the ship, Metaknight runs through the ship, making his way to the Bridge. On the way, he comes across a room that holds Peach's trophy, along with Ness's. He revives them, and they join him. They fight through the ship and eventually find the Bridge, which they find empty. Metaknight takes command of the ship.

At Castle Olrox, Mario and the others stumble across an underground cavern full of pools of strange green liquid. Mewtwo examines one. Deoxys bursts from a pool behind them, and they fight him.

Deoxys is defeated, but he shoots his tentacles at Mewtwo and pulls him in. Deoxys becomes a gelatinous form and consumes Mewtwo. The two combining, he transforms in Deoxtwo. They are forced to fight him. They defeat him; Deoxys is destroyed, but Mewtwo survives. Deoxys's defeat set off a Darkness Bomb that was planted inside his body. The group barely makes it out before Castle Olrox itself is consumed in Darkness.

Meanhile, Billy Hatcher is riding along on his egg. Then he sees a mountain to his left. He sees a small round black object, notifies it then runs. 5 Sec. later the mountain explodes with lava. A small black object lands toward him. he sees a dark man with a ball head (Dark Bomberman) and engages in battle. afterward Dark Bomberman vanishes into a Darkness Bomb. and the REAL Bomberman and mistakes him for the same. Afterwards he's convinced he is good. Billy hatches his eg into a penguin and they slide away.